Shadow Alchemist
by Wind-Mage-Vaati12
Summary: Shadow Link escapes from Vaati and Ganon into Amestris. He meets Edward and Alphonse Elric. To survive and avoid getting captured by his masters he needs to become a State Alchemist. Will he be able to do so and kill his masters? Or will he be caught and serve for the rest of eternity?
1. Chapter 1

**Shadow Alchemist**

**Disclaimer- I do not own Legend of Zelda or Fullmetal Alchemist.**

**Chapter 1- Escape From Hell**

No wind blew, no light shone. Darkness was all that surrounded. The only sound that was heard was commotion in the castle. A short boy with purple hair and pale skin ran through the halls. He tripped and fell. Struggling to his feet he looked back. A dark violet figure flew towards him glaring.

"Get back here Shadow Link!"

Shadow Link stood up and ran. He reached the door and threw it open. He ran across the plain and to a portal. The violet figure kept coming.

"You won't escape me!"

Shadow ran into the portal, and with one last look at his master he blacked out.

…

Vaati looked at Shadow Link disappearing into the portal.

_Curses! The shadow escaped! Master ganon will not be pleased._

**Sorry the chapter is short. I needed to just get it started. The chapters will be longer in the future. I promise!**


	2. Chapter 2

**Shadow Alchemist**

**Disclaimer- I do not own Legend of Zelda or Fullmetal Alchemist. **

**P.S.- The story is going to be sometimes from Shadow Link's point of view, or from Edward's. Sometimes even from Vaati's.**

**Chapter 2- The Fullmetal Alchemist and the Shadow. **

**Shadow's POV**

****I woke up in laying down on a stone floor. Panic raced through my head. Was I back in the castle? In a prison maybe? Were Vaati and Ganon going to kill me? Then I realized that there were other sounds: People, lots of them. I opened my eyes and realized that I was in an alley. I turned my head and saw a crowd of people wearing the strangest clothing I've ever seen. A boy with blond hair and wearing black walked past and stopped. He turned to me and looked into my eyes. He yelled something to someone else than ran towards me. He stopped and sat down next to me.

"You OK?"

I just stared at him. The golden eyed blond smiled and helped me sit up, and leaned me against the wall. A man in a suit of armor walked up to us.

"Brother who is this?"

"I don't know Alphonce."

"Is he injured? If he is, then we should take him back to Central. Right Edward?"

The blond, known as Edward nodded. Stepping away, Alphonce lifted me up. My body was limp and weak.

"W-why are you helping me?" I asked in a raspy voice.

Edward looked at me.

"We help anyone in need. Al prop his head up."

Alphonce did so, and I could see where we were walking now. Edward looked up at me.

"What's your name?"

"Shadow Link. Just Shadow for short."

Edward tilted his head.

"What a strange name. Mine is Edward Elric the Fullmetal Alchemist!" he said, with a huge smile on his face.

I looked at the one carrying me.

"What is your name?" I asked.

"I'm Alphonce Elric. But you can call me Al for short."

I nodded weakly. Then my eyes closed and everything went black.

(Time Skip)

"Edward what happened?!"

"I don't know!"

"What do you mean you don't know?"

"I mean I don't know Winry! I just found Shadow in an alley."

"Shut up." I said.

The voices stopped. My eyes opened and I found myself on a soft bed. Edward and another girl, looked at me. The girl rushed over to me, and stuck her face very close to mine. I scooted back a bit.

"Please don't get so close to me." I whimpered.

She smiled and sat down next to me on the bed.

"Hi I'm Winry. Edward told me your name was Shadow."

I nodded.

"Why are you so nice to me? I'm not human."

Winry started laughing.

"You must have hit your head too hard. Please rest. I'll get you something to at."

I smiled at her. She was kind to me and so was Edward. I could almost call them my friends. I've never had friends before. In fact I've never truly smiled before. Those were all smiles off evil. My former happiness was not truly happiness. I closed my eyes and fell asleep.


	3. Chapter 3

**Shadow Blood Alchemist**

**Disclaimer- I do not own Legend of Zelda or Fullmetal Alchemist.  
P.S.- I thought of a new name for the story!**

**Chapter 3- Mustang's Request**

**Edward's POV**

I stayed in the hospital room Shadow a bit longer, watching as the poor boy peacefully slept. When he said he wasn't human it unnerved me. Was this true?

_Come to think of it... he does have unnaturally pale skin, and purple hair. Where is he from?_

"Edward? Is something wrong?"

I snapped back to reality and looked at the injured purple haired boy. He looked back at me, with his big blue eyes.

"Well yeah."

"What?"

I looked down trying to find the right words.

"Well it's just that apparently your arm was severely injured and had to be removed, while you were sleeping."

He stared at me with wide eyes. Then he looked at where his right arm used to be. Then threw his head into the pillow. Suddenly the door opened and a man walked in. I scowled. It was Colonel Roy Mustang.

"Hello Fullmetal." said Mustang.

"What do you want Mustang?"

Mustang looked at Shadow and smiled.

"I wanted to offer this young man a spot in our army."

"WHAT?!" I yelled.

"This boy needs to survive somehow and for some reason I have a feeling this boy is very strong."

Shadow looked at Mustang. He struggled to sit up and lean on the pillow.

"If I may ask sir, what army?" asked Shadow.

I stared at Shadow, and Mustang chuckled.

"You don't need to call me sir just yet. But you will be serving under me soon."

I glared.

"Colonel won't he have to take the test?"

"No the Furor says these are desperate time. All he needs to do is get well."

Shadow looked at the Colonel with fear in his eyes.

"What?" asked the Colonel.

Shadow kept staring.

"I will be serving under you?"

"Yes?"

"So will you be my new master?"

"What?"

"Will you be my new master?"

Mustang and I both stared at Shadow. Then the Colonel laughed.

"No. I need to go. God bye Fullmetal."

The Colonel handed Shadow a box and an envelope. Then left. I walked over to Shadow and sat on the bed next to him. Shadow opened the envelope, and looked at the letter worriedly.

"What's wrong Shadow?"

"Um... I don't like to admit this but I c-can't read."

Shadow put his head down and I saw his eyes tear up.

"It's ok. I'll read it to you."

He looked at me his shiny blue eyes brimming with tears.

"Really?"

"Yep."

I took the letter and prepared to read.

"By the power vested in me I announce Shadow Link as: The Shadow Blood Alchemist."

I looked at Shadow.

"Shadow Blood Alchemist?" he asked.

I nodded and opened the box. I handed him the silver pocket watch. He took it and turned it over and over in his hands. Then he put it by his bed side.

"Thanks Ed."

I smiled at him then stood and left the room.


	4. Chapter 4

**Shadow Blood Alchemist**

**Disclaimer- I do not own Legend of Zelda or Fullmetal Alchemist.  
P.S.- I thought of a new name for the story! **

**Chapter 4- the Unexpected Visitor**

**Vaati's POV**

I walked through the halls of Ganon's Tower. I was still in a bad mood from Shadow Link's escape. But when Ganon wanted to see me I had no choice but to come to his side right away. Finally I reached two large double doors. I knocked on the large black and red doors and they opened at my touch. I walked into a large dark chamber until I was in front of a large throne. I bowed to the ground with my head down in front of Ganon.

"You wanted to see me Master?"

"Yes I did Wind Mage. I have a request for you."

I looked up a bit.

"A request my lord?"

Ganon nodded.

"I want you and my new creation to go to a world called Amestris, to watch Shadow Link and at the right time retrieve him. Understood?"

I stood and nodded. Ganon flicked his wrist and a girl about Shadow's height appeared next to him. I gasped. This girl looked exactly like Princess Zelda but with strange markings on her body(think Ganon's Puppet in Twilight Princess. Only shorter).

"This is Puppet Zelda. She will come with you to Amestris. She is a very precious creation. It took me a lot of magic to make her. So protect her with your life."

"Of course my lord."

Puppet Zelda walked over to me and waited. When I understood she was waiting for me to go and she would follow, I walked out of the chamber.

...

**Shadow's POV**

_I stood on a battle field facing my old opponents: Green, Red, Blue, and Vio. I was slightly bent over from pain. Green had hit me with his sword a few moments before. I stared at Vio with the most frightening glare I could muster. _

_"How could you Vio?! I thought we were friends! I thought I could trust you!" I screamed. _

_He just smiled at me._

_"I was never your friend. I just had to figure out your plans. That's the only reason I put on the act." _

_I felt my eyes brimming with tears, and before I could stop them tears fell down my face like a water fall. Blue grinned._

_"HA! The shadow is crying!_

_I stood._

_"Don't think this is over! I'm done yet!" _

_"Yes it is." said Vio._

_"We're stronger than we were at Hyrule Castle! We're a team!" they said in perfect unison._

_"Curses. I'll kill... EVERY LAST ONE OF YOU!" _

_They all pointed their swords at me._

_"OH FORCE GIVE US LIGHT!" _

_A light enveloped me. I started screaming my head off. The pain. It enveloped my body, both inside and out. It felt like I was being ripped to shreds. Then everything went black._

I woke up screaming. Edward stepped back in pain. He held his head.

_"_Ow. Shadow, you have a hard head."

"Sorry Ed."

I panted and was sweating.

"You were crying and screaming in your sleep."

I looked at Edward.

"I was?"

Edward nodded.

"What were you dreaming about?"

I put my knees to my head.

"About a friend who betrayed me."

I sobbed into my knees.

_Vio. Vio how could you? I thought I could trust you._

Edward put his hand on my shoulder.

"It's ok. Come on let's go out into town and get you some knew clothes. K?"

I nodded and stood up. I followed Ed out of the room and into town.

...

We walked to a small clothing store. I stared in awe at the store. It was so big to me, and so colorful. Suddenly I felt a very familiar aura. I stopped in my tracks.

"What's wrong Shadow?" asked Edward.

I didn't answer, but instead stared at a tall man with long violet hair. He looked at me and smiled. His voice entered my head and I stumbled back.

_Pitiful Shadow. Did you really think you could escape me? _

"No." I muttered.

Lord Vaati started coming over to me. I couldn't move a muscle, I was stuck as I watched the violet haired wind mage come closer. Soon he stood in front of me smiling down at me.

"Then why did you run?"

"I knew Master Ganon would've sent me after the heroes again. I didn't want to face Vio again."

Vaati let out a laugh.

"Your weak."

I glared at him.

"Your here to take me back, aren't you?"

"No. You're safe... for now."

Then he vanished into thin air. Edward stared at me and the spot where Vaati used to be.

"What the hell?"

"Don't ask. Let's just say he's an enemy we need to avoid for now."

Edward nodded, and led me towards the shop.

_Vaati is here. I need to be very careful. _


	5. Chapter 5

**Shadow Blood Alchemist**

**Disclaimer- I do not own Legend of Zelda or Fullmetal Alchemist.  
P.S.- I thought of a new name for the story! **

**Chapter 5- Puppet Zelda**

**Edward's POV**

After a few minutes Shadow came out of the store wearing dark jeans with silver chains, a black shirt with three stacked silver triangles(A silver triforce), dark combat boots, a black leather jacket, and his pocket watch hanging from a belt and stuck in a pocket. I looked him over and nodded. The whole outfit went along with his purple hair,pale skin, and blue eyes nicely.

"Nice. But kinda of goth."

Shadow smiled at me.

"Do you have a problem with my style?"

I laughed and shook my head. I looked him over more closely and noticed a hilt of a sword sticking over his shoulder. I stared at it.

"What?" he asked.

"What's with the sword?"

"Oh this?" he asked pulling out the sword.

"Where I came from I was very good with this."

I nodded and he put the sword away. We walked to the train station since this kid would be traveling with Alphonce and I. Alphonce was waiting for us at the station.

"Brother!"

"Hey Al! Shadow is going to be travelling with us for a while."

Alphonce nodded. The train wasn't here yet so we sat and waited. Suddenly I saw Shadow's eyes widen and his mouth drop open.

"Something wrong Shadow?" I asked.

He pointed over my shoulder. I looked and my mouth also dropped open. Standing there looking at Shadow, was a girl with blond hair. On her head was a pink sun hat, she was wearing a pink sun dress, and pink flats. What freaked me out where that her eyes were yellow and there were strange markings on her pale skin. She smiled at Shadow and walked over. He stood and walked towards her.

"Hello. Are you Shadow Link?"

"Yes. You are?"

The girl giggled.

"My name is Puppet Zelda."

Shadow looked at her for a while.

"I've had enough of this." I said.

I pulled Shadow away from Puppet Zelda. The wind picked up as the train came. I pulled him on and he yelled a good bye to Puppet Zelda.

...

**Puppet Zelda's POV**

****I looked at Shadow being dragged onto the train. Before the door closed I mumbled a spell and a snake only visible to me crawled into Shadow's flesh. When the train left Vaati appeared by my side.

"Did you do it?" he asked.

I nodded.

"The tracking snake is inside him. I will have no problem tracking him."

Vaati nodded, and threw his cape around me. I felt ourselves disappear.


	6. Chapter 6

**Shadow Blood Alchemist**

**Disclaimer- I do not own Legend of Zelda or Fullmetal Alchemist.  
P.S.- I thought of a new name for the story!**

**I forgot to mention in the previous chapters that Shadow's arm was injured and it can't heal. So it was removed. Sorry! I had a lot on my mind and I seem to have missed that part on my written draft. I'm so sorry if you're confused. :(**

**Chapter 6- The Homunculi**

**Shadow's POV**

I was sitting on my knees like a child. I stared out the window at the beautiful landscape whizzing by. Hyrule was only half as lovely.

_Wow! This place is so pretty! Even Hyrule field is boring compared to this place. _

"Hey Shadow."

I turned to Edward who was smiling at me. I blushed when I realized what I must look like right now.

"Yes Ed?"

"You enjoying yourself?" he asked.

I grinned at him and nodded.

"The place where I come from is only half as lovely."

Edward sat forward in his seat and looked at me with intense interest. Embarrassed I sat down normally. Then I looked at Alphonce.

"Hey Alphonce?"

"Yes?"

I paused finding the words.

"Can I ask you a question please?"

Alphonce looked at me and tilted his head slightly to one side in curiosity.

"What's your question?" he asked.

"Why do you always wear that suit of armor? Isn't it hot?"

Edward and Alphonce noticeably stiffened. Alphonce turned away from me, and Edward sat up strait and ran his fingers through his hair.

"Well... uh..." stammered Al.

"Not here. When we get to our destination."

Alphonce stared at his brother. We were silent for the ride.

...

Finally the train screeched to stop at a small station. The Elric brothers and I walked off the train. Well to be a bit more specific I ran to the door and hopped out. A tall blond girl stood there seemingly waiting for us. She ran forward, and I recognized her to be Winry; the girl who was in the hospital with me then left.

"Hey guys!" she said enthusiastically.

"Hey Winry!" said Alphonce cheerily.

"Hey." said Edward in a flat tone.

I just stayed quiet. I was very shy around girls( unless of course it was Princess Zelda). Winry turned to me with a cheery smile. Then we all walked down a dirt path to a house.

...

When we got there Winry sat me down at a table and started measuring my left arm.

_What could she be doing? _I wondered.

When she finished, she stood and went into another room. After a few minutes she came out with a metal arm. I stared at the object she was holding.

"What's that?" I asked.

She smiled and placed the arm on the table.

"This is Auto mail. It's going to be your new arm."

"My new... arm?"

She nodded. Then motioned for Edward to come.

"Hey Ed can you hold him down for me?"

"Sure." he said putting his hands on my shoulders and tightening his grip.


	7. Chapter 7- Flashback

**So um... hey guys. Wind-Mage-Vaati12 here. So um... this is just a prompt I wrote for school. I wanted to share it with you. I guess this is sort of a filler thing, and this won't be a trend or anything. So... this may be the only one. Or this will become a series within a series. Anyway... ENJOY! **

A shadow stood in front of a pedestal containing the all famous Four Sword. He growled as the aura of the sword sunk in. But he had to finish what he started and get this over with. He took a deep breath putting his hands in front of him palms facing the sword. He began to chant in an ancient tongue, and dark energy shot from him surrounding the Four Sword. Finally he stopped chanting and and gasped for breath. The sword started pulsing with dark power and a black cloud seemed to come out of it. The cloud parted and a tall thin teen kneeled on the grounded in front of the sword. He had silky elbow length violet hair, his bangs covering his left eye. His skin is so pale it's nearly white, tinged with a faint lilac glow that complements his hair perfectly. A loose, cape dyed a deep, royal purple-blue cloaks his somewhat thin form, draping over thin shoulders that seem just a little bit too bony to be healthy and fastened at the front with a round, curved golden button. A thigh-length tunic with a simple collar covers his torso, a much lighter shade of purple than the cape, with long sleeves whose slightly-darker-lilac cuffs are decorated with a single stripe each, a curved line in the middle of each stripe pointing up towards his shoulders. The cuff-stripes and collar are both dyed a shade of purple just a few tones above that of the cape. A golden-yellow, metallic belt loops around his skinny waist, its buckle displaying a red, circular design. Puffy red shorts whose form-fitting bottoms bunch in to hug his legs just below each knee. A pair of simple wide-strapped sandals in the same color as his shorts covers his feet. The teen opens his eyes and stands. The shadow notices his eyes are blood red and there is a black t-shaped marking under both.

"Hello Shadow Link." Said the violet teen.

Shadow Link kneeled with his head down.

"Welcome back Lord Vaati." He said.

Vaati smiled a fanged grin.

"Glad to be back."

He walks forward to Shadow Link with a swish of his cape. Shadow stood as his master walked up to him. Vaati put his hand on top of Shadow's head and ruffled his hair playfully. Shadow shied away a bit at this.

"You've done well to free me Shadow."

Shadow smiled and bowed. It was nice to be praised by his superiors sometimes. Vaati started walking towards the entrance to the Four Sword Sanctuary. Shadow ran to catch up to him, and they left the Sanctuary. Out side two guards were waking up from the sleeping spell Shadow had done earlier. The guard on the right saw Vaati and yelled in surprise. The other guard snapped awake and held his sword up to Vaati's neck. Shadow Link took drew his sword, and prepared to fight the guard. He was surprised when the violet sorcerer, put his hand out to stop Shadow. He looked up at his master.

"Master?"

"I want you to stop Shadow Link. I will take care of these insects."

Shadow sheathed his sword and stepped back. Vaati stood still for a minute as the guards advanced. The first guard charged and the Wind Mage flicked his wrist and the guards were throne into opposite walls like rag dolls. Then Vaati beckoned towards Shadow and the shocked servant walked to stand next to his master. Vaati snapped his fingers and they vanished.

...

They appeared in the Tower of Winds and Vaati almost collapsed to the ground out of weakness. Before he hit the ground Shadow Link caught him and helped him stand. Shadow was alarmed to see that his master's face was covered in sweat and his eyes had a misty, deadened look in them.

"M-master?"

Vaati closed his eyes and shook his head. His breathing was ragged and short.

"I-i'm f-fine. Just a bit w-weak from using m-magic s-so early."

"Can you walk sir?"

Vaati gave a small nod, and pushed himself away from Shadow to stand. He took a few steps before falling to his knees. Shadow once again helped his master stand and then helped him to his room.

...

Vaati lay on his bed still taking short ragged breaths.

"Are you alright Gufuu-sama**(1)**?"

Vaati nodded.

"I just need to rest Sābanto no kage**(2)**."

Shadow nodded and walked out of the room to leave his master to rest.

**So... yeah that's it. Hope you enjoyed it. I actually came up with the ideas to put one of these every six chapters. They will sort of explain Shadow's life under Vaati and Ganon before he ran away. Next chapter will have yaoi in it so... FAIR WARNING! DON'T SAY I DIDN'T WARN YOU! Anyway. A new installment of my Zelda Character Interviews will be out soon as well. Thanks for reading and review! **

**Wait! notes! NOTES! I ALMOST FORGOT! HERE THEY ARE! **

**(1) Gufuu means Vaati in Japanese and sama is given to someone of authority. So Gufuu-sama means Lord Vaati in Japanese. **

**(2) Sābanto no kage means Servant Shadow in Japanese. **

**Sorry for the lesson in Japanese. There will be a few of these in this story. Hope you find them interesting. **

**~Wind-Mage-Vaati12 **


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